1 Answer
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See my answer to the metadata question; to remove metadata with an up-to-date ffmpeg, you can simply:

ffmpeg -i input.mp4 -map 0 -map_metadata -1 -c copy output.mp4

As for your actual question: the avconv in the Ubuntu repositories can output H.264, AAC (albeit it doesn't have libfdk_aac, so you'll have to rely on the lacklustre internal ffmpeg AAC encoder), theora video and vorbis audio. I don't know if it supports VP8 video, but if it does then the commands listed in that SU question should work perfectly well.